title: Genome-scale mapping of DNase I hypersensitivity.
abstract: DNase I-seq is a global and high-resolution method that uses the nonspecific endonuclease DNase I to map chromatin accessibility. These accessible regions, designated as DNase I hypersensitive sites (DHSs), define the regulatory features, (e.g., promoters, enhancers, insulators, and locus control regions) of complex genomes. In this unit, methods are described for nuclei isolation, digestion of nuclei with limiting concentrations of DNase I, and the biochemical fractionation of DNase I hypersensitive sites in preparation for high-throughput sequencing. DNase I-seq is an unbiased and robust method that is not predicated on an a priori understanding of regulatory patterns or chromatin features.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
authors.forename: Sam
authors.initials: S
authors.lastname: John
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Sabo
authors.forename: Theresa K
authors.initials: TK
authors.lastname: Canfield
authors.forename: Kristen
authors.initials: K
authors.lastname: Lee
authors.forename: Shinny
authors.initials: S
authors.lastname: Vong
authors.forename: Molly
authors.initials: M
authors.lastname: Weaver
authors.forename: Hao
authors.initials: H
authors.lastname: Wang
authors.forename: Jeff
authors.initials: J
authors.lastname: Vierstra
authors.forename: Alex P
authors.initials: AP
authors.lastname: Reynolds
authors.forename: Robert E
authors.initials: RE
authors.lastname: Thurman
authors.forename: John A
authors.initials: JA
authors.lastname: Stamatoyannopoulos
mesh_terms: D001665:Binding Sites; D002467:Cell Nucleus / Q000235:genetics*; D002843:Chromatin / Q000378:metabolism*; D003850:Deoxyribonuclease I / Q000378:metabolism*; D005786:Gene Expression Regulation; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008967:Molecular Biology / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D002843:Chromatin; D003850:Deoxyribonuclease I